Complete Genome Analysis of Gluconacetobacter Xylinus CGMCC
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BMC Microbiology BioMed Central Research article Open Access A census of membrane-bound and intracellular signal transduction proteins in bacteria: Bacterial IQ, extroverts and introverts Michael Y Galperin* Address: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA Email: Michael Y Galperin* - [email protected] * Corresponding author Published: 14 June 2005 Received: 18 April 2005 Accepted: 14 June 2005 BMC Microbiology 2005, 5:35 doi:10.1186/1471-2180-5-35 This article is available from: http://www.biomedcentral.com/1471-2180/5/35 © 2005 Galperin; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Analysis of complete microbial genomes showed that intracellular parasites and other microorganisms that inhabit stable ecological niches encode relatively primitive signaling systems, whereas environmental microorganisms typically have sophisticated systems of environmental sensing and signal transduction. Results: This paper presents results of a comprehensive census of signal transduction proteins – histidine kinases, methyl-accepting chemotaxis receptors, Ser/Thr/Tyr protein kinases, adenylate and diguanylate cyclases and c-di-GMP phosphodiesterases – encoded in 167 bacterial and archaeal genomes, sequenced by the end of 2004. The data have been manually checked to avoid false- negative and false-positive hits that commonly arise during large-scale automated analyses and compared against other available resources. The census data show uneven distribution of most signaling proteins among bacterial and archaeal phyla. -
The World of Cyclic Dinucleotides in Bacterial Behavior
molecules Review The World of Cyclic Dinucleotides in Bacterial Behavior Aline Dias da Purificação, Nathalia Marins de Azevedo, Gabriel Guarany de Araujo , Robson Francisco de Souza and Cristiane Rodrigues Guzzo * Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 01000-000, Brazil * Correspondence: [email protected] or [email protected]; Tel.: +55-11-3091-7298 Received: 27 December 2019; Accepted: 17 March 2020; Published: 25 May 2020 Abstract: The regulation of multiple bacterial phenotypes was found to depend on different cyclic dinucleotides (CDNs) that constitute intracellular signaling second messenger systems. Most notably, c-di-GMP, along with proteins related to its synthesis, sensing, and degradation, was identified as playing a central role in the switching from biofilm to planktonic modes of growth. Recently, this research topic has been under expansion, with the discoveries of new CDNs, novel classes of CDN receptors, and the numerous functions regulated by these molecules. In this review, we comprehensively describe the three main bacterial enzymes involved in the synthesis of c-di-GMP, c-di-AMP, and cGAMP focusing on description of their three-dimensional structures and their structural similarities with other protein families, as well as the essential residues for catalysis. The diversity of CDN receptors is described in detail along with the residues important for the interaction with the ligand. Interestingly, genomic data strongly suggest that there is a tendency for bacterial cells to use both c-di-AMP and c-di-GMP signaling networks simultaneously, raising the question of whether there is crosstalk between different signaling systems. In summary, the large amount of sequence and structural data available allows a broad view of the complexity and the importance of these CDNs in the regulation of different bacterial behaviors. -
Protein Expression Profile of Gluconacetobacter Diazotrophicus PAL5, a Sugarcane Endophytic Plant Growth-Promoting Bacterium
Proteomics 2008, 8, 1631–1644 DOI 10.1002/pmic.200700912 1631 RESEARCH ARTICLE Protein expression profile of Gluconacetobacter diazotrophicus PAL5, a sugarcane endophytic plant growth-promoting bacterium Leticia M. S. Lery1, 2, Ana Coelho1, 3, Wanda M. A. von Kruger1, 2, Mayla S. M. Gonc¸alves1, 3, Marise F. Santos1, 4, Richard H. Valente1, 5, Eidy O. Santos1, 3, Surza L. G. Rocha1, 5, Jonas Perales1, 5, Gilberto B. Domont1, 4, Katia R. S. Teixeira1, 6 and Paulo M. Bisch1, 2 1 Rio de Janeiro Proteomics Network, Rio de Janeiro, Brazil 2 Unidade Multidisciplinar de Genômica, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil 3 Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil 4 Laboratório de Química de Proteínas, Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil 5 Laboratório de Toxinologia, Departamento de Fisiologia e Farmacodinâmica- Instituto Oswaldo Cruz- Fundac¸ão Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil 6 Laboratório de Genética e Bioquímica, Embrapa Agrobiologia, Seropédica, Brazil This is the first broad proteomic description of Gluconacetobacter diazotrophicus, an endophytic Received: September 25, 2007 bacterium, responsible for the major fraction of the atmospheric nitrogen fixed in sugarcane in Revised: December 18, 2007 tropical regions. Proteomic coverage of G. diazotrophicus PAL5 was obtained by two independent Accepted: December 19, 2007 approaches: 2-DE followed by MALDI-TOF or TOF-TOF MS and 1-DE followed by chromatog- raphy in a C18 column online coupled to an ESI-Q-TOF or ESI-IT mass spectrometer. -
Embracing Bacterial Cellulose As a Catalyst for Sustainable Fashion
Running head: BACTERIAL CELLULOSE 1 Embracing Bacterial Cellulose as a Catalyst for Sustainable Fashion Luis Quijano A Senior Thesis submitted in partial fulfillment of the requirements for graduation in the Honors Program Liberty University Fall 2017 BACTERIAL CELLULOSE 2 Acceptance of Senior Honors Thesis This Senior Honors Thesis is accepted in partial fulfillment of the requirements for graduation from the Honors Program of Liberty University. ______________________________ Debbie Benoit, D.Min. Thesis Chair ______________________________ Randall Hubbard, Ph.D. Committee Member ______________________________ Matalie Howard, M.S. Committee Member ______________________________ David E. Schweitzer, Ph.D. Assistant Honors Director ______________________________ Date BACTERIAL CELLULOSE 3 Abstract Bacterial cellulose is a leather-like material produced during the production of Kombucha as a pellicle of bacterial cellulose (SCOBY) using Kombucha SCOBY, water, sugar, and green tea. Through an examination of the bacteria that produces the cellulose pellicle of the interface of the media and the air, currently named Komagataeibacter xylinus, an investigation of the growing process of bacterial cellulose and its uses, an analysis of bacterial cellulose’s properties, and a discussion of its prospects, one can fully grasp bacterial cellulose’s potential in becoming a catalyst for sustainable fashion. By laying the groundwork for further research to be conducted in bacterial cellulose’s applications as a textile, further commercialization of bacterial cellulose may become a practical reality. Keywords: Acetobacter xylinum, alternative textile, bacterial cellulose, fashion, Komagateibacter xylinus, sustainability BACTERIAL CELLULOSE 4 Embracing Bacterial Cellulose as a Catalyst for Sustainable Fashion Introduction One moment the fashionista is “in”, while the next day the fashionista is “out”. The fashion industry is typically known for its ever-changing trends, styles, and outfits. -
Yeast Genome Gazetteer P35-65
gazetteer Metabolism 35 tRNA modification mitochondrial transport amino-acid metabolism other tRNA-transcription activities vesicular transport (Golgi network, etc.) nitrogen and sulphur metabolism mRNA synthesis peroxisomal transport nucleotide metabolism mRNA processing (splicing) vacuolar transport phosphate metabolism mRNA processing (5’-end, 3’-end processing extracellular transport carbohydrate metabolism and mRNA degradation) cellular import lipid, fatty-acid and sterol metabolism other mRNA-transcription activities other intracellular-transport activities biosynthesis of vitamins, cofactors and RNA transport prosthetic groups other transcription activities Cellular organization and biogenesis 54 ionic homeostasis organization and biogenesis of cell wall and Protein synthesis 48 plasma membrane Energy 40 ribosomal proteins organization and biogenesis of glycolysis translation (initiation,elongation and cytoskeleton gluconeogenesis termination) organization and biogenesis of endoplasmic pentose-phosphate pathway translational control reticulum and Golgi tricarboxylic-acid pathway tRNA synthetases organization and biogenesis of chromosome respiration other protein-synthesis activities structure fermentation mitochondrial organization and biogenesis metabolism of energy reserves (glycogen Protein destination 49 peroxisomal organization and biogenesis and trehalose) protein folding and stabilization endosomal organization and biogenesis other energy-generation activities protein targeting, sorting and translocation vacuolar and lysosomal -
K319-100 Gluconokinase Activity Assay Kit (Colorimetric)
FOR RESEARCH USE ONLY! Gluconokinase Activity Assay Kit (Colorimetric) 7/16 (Catalog # K319-100; 100 assays; Store at -20°C) I. Introduction: Gluconokinase (ATP:D-gluconate 6-phosphotransferase or Gluconate Kinase; EC:2.7.1.12) is a key enzyme for Gluconate degradation pathway. In E. coli and yeast, Gluconokinase can convert gluconate into 6-Phosphate-D-Gluconate in an ATP dependent manner. Through Hexose Monophosphate Shunt (HMS) pathway, 6-Phosphate-D-Gluconate generates ribose-6-phosphate, which is critical for nucleotides and nucleic acid synthesis. Little is known of the mechanism of gluconate metabolism in humans despite its widespread use in medicine and consumer products. BioVision’s Gluconokinase Assay kit provides a quick and easy way for monitoring Gluconokinase activity in a variety of samples. In this kit, Gluconokinase converts Gluconate into 6-Phosphate-D-Gluconate in an ATP dependent manner. 6-Phosphate-D-Gluconate and ADP in turn undergoe a series of reactions to form an intermediate, which reacts with the probe to form a colored product with strong absorbance (OD 450 nm). The assay is simple, sensitive, and high-throughput adaptable. Detection limit: < 0.1mU. Gluconokinase D-Gluconate + ATP 6-Phosphate-D-Gluconate + ADP Intermediate + Probe Color Product (OD 450 nm) II. Application: Measurement of Gluconokinase activity in various samples Mechanistic study of Pentose Phosphate Pathway III. Sample Type: Prokaryote such as: E.coli Animal tissues such as liver, kidney, etc. Adherent or suspension cells. IV. Kit Contents: Components K319-100 Cap Code Part Number Gluconokinase Assay Buffer 25 ml WM K319-100-1 Gluconokinase Substrate 1 Vial Blue K319-100-2 ATP 1 Vial Orange K319-100-3 Gluconokinase Converting Enzyme 1 Vial Purple K319-100-4 Gluconokinase Developer 1 Vial Green K319-100-5 Gluconokinase Probe 1 Vial Red K319-100-6 NADH Standard 1 Vial Yellow K319-100-7 Gluconokinase Positive Control 1 Vial Brown K319-100-8 V. -
Dissection of Exopolysaccharide Biosynthesis in Kozakia Baliensis Julia U
Brandt et al. Microb Cell Fact (2016) 15:170 DOI 10.1186/s12934-016-0572-x Microbial Cell Factories RESEARCH Open Access Dissection of exopolysaccharide biosynthesis in Kozakia baliensis Julia U. Brandt, Frank Jakob*, Jürgen Behr, Andreas J. Geissler and Rudi F. Vogel Abstract Background: Acetic acid bacteria (AAB) are well known producers of commercially used exopolysaccharides, such as cellulose and levan. Kozakia (K.) baliensis is a relatively new member of AAB, which produces ultra-high molecular weight levan from sucrose. Throughout cultivation of two K. baliensis strains (DSM 14400, NBRC 16680) on sucrose- deficient media, we found that both strains still produce high amounts of mucous, water-soluble substances from mannitol and glycerol as (main) carbon sources. This indicated that both Kozakia strains additionally produce new classes of so far not characterized EPS. Results: By whole genome sequencing of both strains, circularized genomes could be established and typical EPS forming clusters were identified. As expected, complete ORFs coding for levansucrases could be detected in both Kozakia strains. In K. baliensis DSM 14400 plasmid encoded cellulose synthase genes and fragments of truncated levansucrase operons could be assigned in contrast to K. baliensis NBRC 16680. Additionally, both K. baliensis strains harbor identical gum-like clusters, which are related to the well characterized gum cluster coding for xanthan synthe- sis in Xanthomanas campestris and show highest similarity with gum-like heteropolysaccharide (HePS) clusters from other acetic acid bacteria such as Gluconacetobacter diazotrophicus and Komagataeibacter xylinus. A mutant strain of K. baliensis NBRC 16680 lacking EPS production on sucrose-deficient media exhibited a transposon insertion in front of the gumD gene of its gum-like cluster in contrast to the wildtype strain, which indicated the essential role of gumD and of the associated gum genes for production of these new EPS. -
Cellulose Digestion and Metabolism Induced Biocatalytic Transitions in Anaerobic Microbial Ecosystems
Metabolites 2014, 4, 36-52; doi:10.3390/metabo4010036 OPEN ACCESS metabolites ISSN 2218-1989 www.mdpi.com/journal/metabolites/ Article Cellulose Digestion and Metabolism Induced Biocatalytic Transitions in Anaerobic Microbial Ecosystems Akira Yamazawa 1,2, Tomohiro Iikura 2, Yusuke Morioka 2, Amiu Shino 3, Yoshiyuki Ogata 4, Yasuhiro Date 2,3 and Jun Kikuchi 2,3,5,6,* 1 Research Planning and Management Group, Kajima Technical Research Institute, Kajima Corporation, 2-19-1 Tobitakyu, Chofu, Tokyo 182-0036, Japan; E-Mail: [email protected] 2 Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehirocho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; E-Mails: [email protected] (T.I.); [email protected] (Y.M.); [email protected] (Y.D.) 3 RIKEN Center for Sustainable Resource Science, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; E-Mail: [email protected] (A.S.) 4 Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka 599-8531, Japan; E-Mail: [email protected] 5 Graduate School of Bioagricultural Sciences, Nagoya University, 1 Furo-cho, Chikusa-ku, Nagoya, Aichi 464-0810, Japan 6 RIKEN Biomass Engineering Program, 2-1 Hirosawa, Wako 351-0198, Japan * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +81-45-503-9439; Fax: +81-45-503-9489. Received: 13 September 2013; in revised form: 18 December 2013 / Accepted: 20 December 2013 / Published: 31 December 2013 Abstract: Anaerobic digestion of highly polymerized biomass by microbial communities present in diverse microbial ecosystems is an indispensable metabolic process for biogeochemical cycling in nature and for industrial activities required to maintain a sustainable society. -
Complete Genome Sequence and Methylome Analysis of Beggiatoa Leptomitoformis Strains D-401 and D-402
Complete Genome Sequence and Methylome Analysis of Beggiatoa leptomitoformis strains D-401 and D-402. Alexey Fomenkova*, Zhiyi Suna Tamas Vinczea, Maria Orlova b, Brian P. Antona, Margarita Yu. Grabovichb, Richard J. Roberts a. aNew England Biolabs, Ipswich, MA, USA bDepartment of Biochemistry and Cell Physiology, Voronezh State University, Voronezh, Russia. *Correspondence: [email protected] The taxonomy of Beggiatoa genus is still a work in progress. Despite many morphotypes of the Beggiatoa genus having been described in the literature, only one species, B. alba has been validated until now. In 2016, we described a second species, B. leptomitoformis. Two strains of B. leptomitoformis D-401 and D-402 have been isolated from different regions of Russia. They differ in their morphology and physiology and especially their ability to grow lithotrophically in the presence of thiosulfate. While B. leptomitoformis D-402 is able to accumulate elemental sulfur, strain D-401 cannot. We performed genomic sequencing of these two strains using the PacBio SMRT platform and assembled the reads into two complete circular genomes: B. leptomitoformis D-401 with 4,266,286 bp and D-402 with 4,265,296 bp. Both genome sequences have been deposited in GenBank with accession numbers CP018889 and CP012373 respectively (1). Surprisingly these two genomes showed almost 99% identity. The preliminary analysis of metabolic operons of thiosulfate oxidation (soxAXBZY) and autotrophic assimilation of CO2 (the genes encoded for the enzymes of the Calvin-Bassham cycle) in both strains did not reveal any noticeable differences. One advantage of the PacBio sequencing platform is its ability to detect the epigenetic state of the sequenced DNA, which allows for the identification of modified nucleotides and the corresponding motifs in which they occur. -
Bacterial Cellulose - Properties and Its Potential Application (Bakteria Selulosa - Sifat Dan Keupayaan Aplikasi)
Sains Malaysiana 50(2)(2021): 493-505 http://dx.doi.org/10.17576/jsm-2021-5002-20 Bacterial Cellulose - Properties and Its Potential Application (Bakteria Selulosa - Sifat dan Keupayaan Aplikasi) IZABELA BETLEJ, SARANI ZAKARIA, KRZYSZTOF J. KRAJEWSKI & PIOTR BORUSZEWSKI* ABSTRACT This review paper is related to the utilization on bacterial cellulose in many applications. The polymer produced from bacterial cellulose possessed a very good physical and mechanical properties, such as high tensile strength, elasticity, absorbency. The polymer from bacterial cellulose has a significantly higher degree of polymerization and crystallinity compared to those derived from plant. The collection of selected literature review shown that bacterial cellulose produced are in the form pure cellulose and can be used in many of applications. These include application in various industries and sectors of the economy, from medicine to paper or electronic industry. Keywords: Acetobacter xylinum; biocomposites; culturing; properties of bacterial cellulose ABSTRAK Ulasan kepustakaan ini adalah mengenai bakteria selulosa yang digunakan dalam banyak aplikasi. Bahan polimer yang terhasil daripada bakteria selulosa mempunyai sifat fizikal dan mekanikal yang sangat baik seperti sifat kekuatan regangan, kelenturan dan serapan. Bahan polimer terhasil daripada selulosa bakteria mempunyai darjah pempolimeran dan kehabluran yang tinggi berbanding daripada sumber tumbuhan. Suntingan kajian daripada beberapa koleksi ulasan kepustakaan menunjukkan bakteria selulosa terhasil adalah selulosa tulen yang boleh digunakan untuk banyak kegunaan. Antaranya adalah untuk pelbagai industri dan sektor ekonomi seperti perubatan atau industri elektronik. Kata kunci: Acetobacter xylinum; komposit-bio; pengkulturan; sifat bakteria selulosa INTRODUCTION Yamada et al. 2012). The first reports on the synthesis of Cellulose is the most common polymer found in nature. -
Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase -
Evidence for Extensive Heterotrophic Metabolism, Antioxidant Action, and Associated Regulatory Events During Winter Hardening In
Collakova et al. BMC Plant Biology 2013, 13:72 http://www.biomedcentral.com/1471-2229/13/72 RESEARCH ARTICLE Open Access Evidence for extensive heterotrophic metabolism, antioxidant action, and associated regulatory events during winter hardening in Sitka spruce Eva Collakova1, Curtis Klumas2, Haktan Suren2,3,ElijahMyers2,LenwoodSHeath4, Jason A Holliday3 and Ruth Grene1* Abstract Background: Cold acclimation in woody perennials is a metabolically intensive process, but coincides with environmental conditions that are not conducive to the generation of energy through photosynthesis. While the negative effects of low temperatures on the photosynthetic apparatus during winter have been well studied, less is known about how this is reflected at the level of gene and metabolite expression, nor how the plant generates primary metabolites needed for adaptive processes during autumn. Results: The MapMan tool revealed enrichment of the expression of genes related to mitochondrial function, antioxidant and associated regulatory activity, while changes in metabolite levels over the time course were consistent with the gene expression patterns observed. Genes related to thylakoid function were down-regulated as expected, with the exception of plastid targeted specific antioxidant gene products such as thylakoid-bound ascorbate peroxidase, components of the reactive oxygen species scavenging cycle, and the plastid terminal oxidase. In contrast, the conventional and alternative mitochondrial electron transport chains, the tricarboxylic acid cycle, and redox-associated proteins providing reactive oxygen species scavenging generated by electron transport chains functioning at low temperatures were all active. Conclusions: A regulatory mechanism linking thylakoid-bound ascorbate peroxidase action with “chloroplast dormancy” is proposed. Most importantly, the energy and substrates required for the substantial metabolic remodeling that is a hallmark of freezing acclimation could be provided by heterotrophic metabolism.